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(-) Description

Title :  BTK IN COMPLEX WITH GDC-0834
 
Authors :  A. S. Gardberg
Date :  20 Sep 16  (Deposition) - 24 May 17  (Release) - 24 May 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.71
Chains :  Asym./Biol. Unit :  A
Keywords :  Lead Optimization, Protein Kinase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. T. Bender, A. Gardberg, A. Pereira, T. Johnson, Y. Wu, R. Grenningloh, J. Head, F. Morandi, P. Haselmayer, L. Liu-Bujalski
Ability Of Bruton'S Tyrosine Kinase Inhibitors To Sequester Y551 And Prevent Phosphorylation Determines Potency For Inhibition Of Fc Receptor But Not B-Cell Receptor Signaling
Mol. Pharmacol. V. 91 208 2017
PubMed-ID: 28062735  |  Reference-DOI: 10.1124/MOL.116.107037

(-) Compounds

Molecule 1 - TYROSINE-PROTEIN KINASE BTK
    Chains: A
    EC Number: 2.7.10.2
    Engineered: YES
    Expression System: TRICHOPLUSIA NI
    Expression System Strain: HI5
    Expression System Taxid: 7111
    Fragment: KINASE DOMAIN
    Gene: BTK, AGMX1, ATK, BPK
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: AGAMMAGLOBULINEMIA TYROSINE KINASE,ATK,B-CELL PROGENITOR KINASE,BPK,BRUTON TYROSINE KINASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric/Biological Unit (3, 6)
No.NameCountTypeFull Name
12VL1Ligand/IonN-{3-[6-({4-[(2R)-1,4-DIMETHYL-3-OXOPIPERAZIN-2-YL]PHENYL}AMINO)-4-METHYL-5-OXO-4,5-DIHYDROPYRAZIN-2-YL]-2-METHYLPHENYL}-4,5,6,7-TETRAHYDRO-1-BENZOTHIOPHENE-2-CARBOXAMIDE
2EDO4Ligand/Ion1,2-ETHANEDIOL
3GOL1Ligand/IonGLYCEROL

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:407 , LEU A:408 , PHE A:413 , VAL A:416 , ALA A:428 , LYS A:430 , THR A:474 , GLU A:475 , TYR A:476 , MET A:477 , ALA A:478 , GLY A:480 , ASN A:526 , LEU A:528 , ASP A:539 , TYR A:551 , HOH A:962binding site for residue 2VL A 701
2AC2SOFTWARETYR A:598 , GLU A:599 , ARG A:600 , PHE A:601 , HOH A:807 , HOH A:884 , HOH A:941binding site for residue EDO A 702
3AC3SOFTWAREARG A:520 , ASP A:521 , LEU A:522 , TRP A:563 , SER A:564 , ALA A:582 , HOH A:836 , HOH A:885 , HOH A:902binding site for residue EDO A 703
4AC4SOFTWAREGLU A:599 , ARG A:600 , LYS A:645binding site for residue EDO A 705
5AC5SOFTWAREPHE A:404 , LEU A:405 , LYS A:406 , GLU A:407 , LYS A:417 , HOH A:851binding site for residue GOL A 706

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5P9F)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Arg A:468 -Pro A:469

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5P9F)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5P9F)

(-) Exons   (0, 0)

(no "Exon" information available for 5P9F)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:266
                                                                                                                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhh.eeeeeeeeee..eeeeeeee...eeeeeee......hhhhhhhhhhhhh.........eeeee......eeee......hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh.......hhh.eee.....eee...hhhhhh.hhhhhh......hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.........hhhhhhhhhhh..........hhhhhhhhhhh...hhhhh.hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5p9f A 394 SWEIDPKDLTFLKELGTGQFGVVKYGKWRGQYDVAIKMIKEGSMSEDEFIEEAKVMMNLSHEKLVQLYGVCTKQRPIFIITEYMANGCLLNYLREMRHRFQTQQLLEMCKDVCEAMEYLESKQFLHRDLAARNCLVNDQGVVKVSDFGLSRYVLDDEYTSSVGSKFPVRWSPPEVLMYSKFSSKSDIWAFGVLMWEIYSLGKMPYERFTNSETAEHIAQGLRLYRPHLASEKVYTIMYSCWHEKADERPTFKILLSNILDVMDEES 659
                                   403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613       623       633       643       653
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 5P9F)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5P9F)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5P9F)

(-) Gene Ontology  (49, 49)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Arg A:468 - Pro A:469   [ RasMol ]  
 

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  5p9f
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Access by UniProt ID/Accession number
  BTK_HUMAN | Q06187
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  2.7.10.2
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        BTK_HUMAN | Q06187: 1aww 1awx 1b55 1btk 1bwn 1k2p 1qly 2ge9 2z0p 3gen 3k54 3ocs 3oct 3p08 3pix 3piy 3piz 3pj1 3pj2 3pj3 4nwm 4ot5 4ot6 4otf 4otq 4otr 4rfy 4rfz 4rg0 4rx5 4yhf 4z3v 4zly 4zlz 5bpy 5bq0 5fbn 5fbo 5j87 5jrs 5kup 5p9g 5p9h 5p9i 5p9j 5p9k 5p9l 5p9m 5t18 5u9d 5vgo

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5P9F)